BioC 3.4: CHECK report for edgeR on zin1

Package: edgeR

Version: 3.15.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.15.2.tar.gz

StartedAt: 2016-09-20 05:56:33 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:57:31 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 58.4 seconds

RetCode: 0

Status:  OK

CheckDir: edgeR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings edgeR_3.15.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/edgeR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘edgeR/DESCRIPTION’ ... OK
* this is package ‘edgeR’ version ‘3.15.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘edgeR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘edgeR-Tests.R’
  Comparing ‘edgeR-Tests.Rout’ to ‘edgeR-Tests.Rout.save’ ... OK
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘edgeR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_compute_nbdev.cpp -o R_compute_nbdev.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_levenberg.cpp -o R_levenberg.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_loess_by_col.cpp -o R_loess_by_col.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_one_group.cpp -o R_one_group.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c adj_coxreid.cpp -o adj_coxreid.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c fmm_spline.c -o fmm_spline.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c glm_levenberg.cpp -o glm_levenberg.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c glm_one_group.cpp -o glm_one_group.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c interpolator.cpp -o interpolator.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c matvec_check.cpp -o matvec_check.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c nbdev.cpp -o nbdev.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o edgeR.so R_compute_nbdev.o R_cr_adjust.o R_exact_test_by_deviance.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/edgeR.Rcheck/edgeR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (edgeR)

name	user	system	elapsed
DGEList	0.016	0.000	0.017
WLEB	0.020	0.000	0.023
adjustedProfileLik	0.008	0.000	0.009
aveLogCPM	0.000	0.000	0.003
binomTest	0.000	0.000	0.002
calcNormFactors	0.004	0.000	0.004
camera.DGEList	0.136	0.000	0.135
commonCondLogLikDerDelta	0.004	0.000	0.002
condLogLikDerSize	0.000	0.000	0.001
cpm	0.000	0.000	0.002
cutWithMinN	0.004	0.000	0.002
dglmStdResid	0.012	0.000	0.013
diffSpliceDGE	0.068	0.000	0.072
dim	0.000	0.000	0.002
dispBinTrend	0.484	0.004	0.484
dispCoxReid	0.028	0.000	0.028
dispCoxReidInterpolateTagwise	0.044	0.000	0.044
dispCoxReidSplineTrend	0.788	0.000	0.788
dropEmptyLevels	0.004	0.000	0.001
edgeRUsersGuide	0.000	0.000	0.001
equalizeLibSizes	0.02	0.00	0.02
estimateCommonDisp	0.036	0.000	0.035
estimateDisp	0.252	0.000	0.249
estimateExonGenewisedisp	0.012	0.000	0.014
estimateGLMCommonDisp	0.080	0.000	0.083
estimateGLMRobustDisp	0.688	0.000	0.686
estimateGLMTagwiseDisp	0.156	0.000	0.156
estimateGLMTrendedDisp	0.116	0.004	0.118
estimateTagwiseDisp	0.044	0.000	0.045
estimateTrendedDisp	0.324	0.000	0.321
exactTest	0.008	0.000	0.010
expandAsMatrix	0	0	0
getCounts	0.008	0.000	0.008
getPriorN	0.004	0.000	0.002
gini	0.000	0.000	0.001
glmQLFTest	0.552	0.000	0.552
glmTreat	0.020	0.000	0.021
glmfit	0.048	0.000	0.048
goana	0	0	0
gof	0.012	0.000	0.013
goodTuring	0.008	0.000	0.008
loessByCol	0.004	0.000	0.002
maPlot	0.016	0.000	0.016
maximizeInterpolant	0.004	0.000	0.001
maximizeQuadratic	0.000	0.000	0.001
meanvar	0.072	0.004	0.074
mglm	0.008	0.000	0.009
movingAverageByCol	0.000	0.000	0.001
nbinomDeviance	0	0	0
plotBCV	0.512	0.000	0.513
plotExonUsage	0.004	0.000	0.007
plotMDS.DGEList	0.020	0.000	0.019
plotQLDisp	0.556	0.004	0.561
plotSmear	0.524	0.000	0.523
predFC	0.012	0.000	0.012
q2qnbinom	0.000	0.000	0.001
readDGE	0.004	0.000	0.000
roast.DGEList	0.132	0.000	0.135
romer.DGEList	4.536	0.000	4.539
spliceVariants	0.012	0.000	0.013
splitIntoGroups	0.000	0.000	0.002
subsetting	0.012	0.000	0.013
sumTechReps	0.000	0.000	0.001
systematicSubset	0	0	0
thinCounts	0.000	0.000	0.001
topTags	0.020	0.000	0.018
validDGEList	0.000	0.000	0.002
weightedCondLogLikDerDelta	0.000	0.000	0.002
zscoreNBinom	0.004	0.000	0.000